Project Heretic
by lilfoxkit
Summary: Like many magic bullet projects of the great war, Project Freelancer was discontinued, but what about the other programs, like Project Heretic and Project Recycle? Well in this novel we shall find out! Centered around the Freelancers for the most part with background from Reds and Blues, gets much better after chapter 1! Updates will be weekly - monthly.
1. Chapter 1

Disclaimer: I don't own a motherfucking thing.

(Special note: This takes place after season 10)

One last thing, while Project Heretic and Project Recycle are of my own creation, Dr. Han is not, she is from Jaden Silver's story Chemical Imbalance, which will be linked at the end of this story. It's been a huge inspiration to this story. Someone else I would like to thank is nursehelena a famous Metaloclypse fan fiction writer who helps boast that community to a large degree and has written dozens of amazing stories. With both of these authors help I was able to plan and write out the story I had pictured in my head. Oh and I wrote this out in

"Breaking news! The UNSC has found the body of the deceased Dr. Church of the infamous Project Freelancer; for those of you who are unaware, the Office of Naval Intelligence had various Special Operations programs during the Great War such as the famous Spartan – II program, though Project Freelancer's Director was found to have tortured its' given AI causing it to fragment. These horrific acts have been brought to the United Nations attention, only to have various new laws passed rather quickly. They are referred to "Churches laws" in reference to the ethical and legal use of AI's in a militar-"

Glancing away from the video feed, a chill went down spine Major Reclin as he peered down at his holo-tablet; he had received a subpoena from his commanding officer this evening ordering a report about his involvement with an old associate by the name of Dr. Han. Like him, she was the Director of one of the many magic bullet programs from the war. She had become a war criminal and was the most recent target of the UNSC. It was a shame really, they both studied psychology at one of Earths' more prestigious universities together. To the Majors knowledge, her project was deemed a huge failure when she used her agents to attack innocent colonies.

Tapping his index finger against the blinking light of his tablet, his aged face felt a smile engrain itself. Standing up, the officer walked out of his dimly lit room, only to halt at a sealed door. With a soft hiss, the door slid open, allowing the Major to enter; looking around at the two beings strapped against two sterile looking operating tables, one resembled a rather large gray, leathery skinned creature who was struggling against his restraints like a madman, while its companion stared silently at the doctor. The second being was of a much more human nature, appearing to be in his late forties; his name was Senior Master Sergeant Dylan T. Derara, USNC Air Force.

"It's good to see you again mi Mayor." Derara paused; catching himself speaking in a way that he knew irritated the Major. Blinking a few times, he continued in a monotone. "Is there something you require of Number 443 and Number 444 today?"

Major Reclin rather enjoyed number 443, he considered the Sergeant to be one of his better creations from Project Heretic. He could never break the man of using Spanish words mixed in with English, not that it was a bad thing; it helped the Major consider that there may have been hope of rehabilitating his men someday.

"Oh, nothing today Dylan, just some routine inspections of your cybernetic implants after all, I can't have those malfunctioning, can I?"

The brainwashed soldier responded by closing his eyes and waiting for the Major to perform the surgery, while he only needed to check one of them; 443 and 444 couldn't be very far away from one another for very long or the repercussions would be bad. The Major picked up a sharp looking scalpel, only to place it rather swiftly against the man's head. As blood oozed onto the floor, both humans remained deathly still as the screams of the Sangheili echoed throughout the room; grunting, the Major peeled back the skin with his bare fingers. Throughout the muscles of the airman's skull, various metallic devices could be seen, some branching out in a tentacle-like fashion, others stopping abruptly to make a cracked spider web pattern.

"All right Sergeant, everything appears to be functioning correctly." As he spoke, blood splattered onto Reclins' shoes, causing him to wrinkle his nose in disgust.

"Thank you sir, Number 443 requesting medical assistance. Status: Number 443 has minor head wound losing and losing blood pressure." Said 443 in an empty voice.

"Of course, my apologizes." Cringing, he looked at the abomination before him as he picked up a circular device.

Pulling the trigger, the device began to glow a queer green color while the wound started to heal up at a rather rapid pace. Leaning over Sergeant Derara's body, he released the restraints upon the man, leaving the soldier to release his partner as he exited the room. Pacing back over to his desk, the Major glanced down at his tablet once again, yet another message though this time, the Major wasn't expecting anything.

Tapping it open, bright large white words flashed on the screen. "THEY ARE ON THEIR WAY STOP.

RUN STOP."

The Majors' face turned pale in color; He had been found. He always knew his job would catch up with him one day. Still, he had time before the organization arrived, or at least he hoped he did. The Major was stationed out on an Arctic based planet, being contained within an older military base that had been recycled to him for his research and Project Heretic as a whole. The base was created during the Great War as an observational post, only to be transformed into a training facility, then finally a research laboratory.

As the blood rushed back into the Majors' face, he quietly walked into the laboratory, seeing that the pair bond were standing at attention. "Gear up, we are leaving base." At the Majors word, the alien and human bolted out of the surgical room at inhuman speeds. The Major had other things to attend to before they could leave such as copying over data, shutting down the facility and preparing an escape vehicle.

Rushing over to a nearby computer console, the Major quickly typed in select commands into the holographic keyboard; instantly, the screen lit up in a blaze of colors, swirling around in a small dance as the pixels shifted. Then, just as quick as it came, the screen faded into a black color indicating that the system had been shut down. He had to hurry, if he was found, everything he fought for would be lost; the doors to his personal office opened as 443 and 444 stood once more at attention in their BDUs'.

"Sir, before system destruction, sensors indicate that enemy eta is twenty minutes. Orders?"

"I need you and T-3 to prepare for evacuation, I shall join you in five."

"Ci, mi Mayor."

Just after the duo left, a loud explosion echoed throughout the base; the enemy had arrived sooner than expected. Muttering a curse under his breath, the Major quickly began sphering the remaining data from his holo-tablet into his implants, urging it to go faster despite the physical impossibility. More rumbles were heard throughout the base as the last of the data transferred. With great haste, the Major ran out into the vehicle bay and occupied a Pelican-class drop ship; with the Director on board, the engines fired up and skirted out of the base, barely missing the enemy soldiers entering the bay.

Looking over at the beast sitting in the seat next to him, the Major placed a gentle hand upon its head.

"Well T-3, it looks like we are on the move again."

In response the alien let out a soft whining noise as it nuzzled against the Majors hand. Reclin let out a long sigh, even with what little support their group had, he had a bad feeling about the future to come.

So not a very strong chapter, but it has been a long time since I've wrote anything. As promised, a link to Jaden Silvers story: s/9915518/1/Chemical-Imbalance


	2. Will you do me the honor?

**Disclaimer, I don't own shit!**

**Again, my thanks to my Beta and for this chapter particularly, Jaden Silver, who is just fucking awesome!**

A swirling dark void was the only thing he was aware of as it enveloped him, embracing his entire being; a feeling of warmth spread all throughout his body, only to rescind into the center and back out again. The warmth would occasionally spread out farther than his physical body could manifest, though somehow he knew it was there.

Suddenly, bright flashes of colors blurred across his vision, only for a hulking entity to come into focus and fade away just as quickly as it came; then a thought occurred to him.

He didn't know where he was or how he got there.

He couldn't remember his name either.

He tried to focus on one thing, one thing only, amidst the thousand swirling questions, thinking, reaching out into what memories he could muster, yet to no avail.

What was it?

Oh right, his name was Benjamin.

It was at this point he noticed something, something that had been going on for quite some time now from the corner of his eye. There had been a small white light and every so often it would get a little bigger, then a bit bigger and now it was all he could see.

And then, there it was, he was finally awake. Instant recognition drew over him when he realized there was a large amount of fluid in his ears, even so there was something else. It was muffled but it was there.

"...don't know Doctor, they both have extensive damage..."

That was all he could pick up as the fluid drained from his ears and though he couldn't will his eyelids open just yet, he managed to strain his ears to hear a little more.

"…silly, they are ready. And even if they're not, we need them."

Forcing his eyes open with a rather harsh push, he was greeted with the slightly blurred image of his own naked, muscular body against a metal table. It then occurred to him for the first time that he was in a very cold environment, feeling goose bumps forming on his arms. Curling his brow, he saw that one of the men standing over him was smiling at him.

"Ah, boyo, you're awake. It was touch and go for a while there; you're a very lucky young man. Now hold still this might hurt a little as I was hopin' that ye'd be asleep for a wee bit longer."

Suddenly he felt a large amount of pin pricks throughout his biceps and torso; his instant reaction was to curl his body in defense.

"Hey, hey, easy now, it will be over in a minute."

As strange as it was, the speaker's voice had a calming effect. Opening his mouth to speak, Ben felt the painful acid of his stomach tract usher up to his throat. Forcing it back down, a sharp pain shot though his arm while his mind went blank.

Several hours later, Ben opened his eyes after awaking from his medically induced coma. Letting out a low groan, the man placed a hand against his head. He opened his eyes and looked around only to see a much different environment. Instead of a cold and harsh lighting of the previous room, he was now in a hospital bed with warm blankets draped over him. Several monitors were scattered about, some unplugged, but for the most part, he saw that they were hooked up to him in some manner.

"What the…" He said, tracing the wires that scaled down his arm with aggressive vigor.

"I wouldn't touch that if I were you," a confusingly familiar voice called out. "I'm pretty sure it was put there for a reason."

He looked around, unable to see the owner of the voice itself. Instead, Ben saw a large curtain separating him from the speaker, a small, shadowy outline of the human body being the only indicator there was anything there at all though the man did seem very familiar.

The silhouette matched with the voice tugged at something in his memory, and he strained to grasp what it was.

"Eugene?" he finally asked, the illusive thought finally captured in his mind.

"Good to see your brain is still functioning Ben," the other man said, compassionate voice calmingly familiar to Ben. "Although to be fair, I honestly thought we would never see each other again," Eugene continued. "Not after what happened with the Director and everything."

"Where are we?" Ben asked, trying and failing to sit up. He glanced around the room, noting that it was definitely not the infirmary aboard the Mother of Invention.

"I'm not sure," Eugene answered honestly, "but I'll tell you what I've figured out so far. I saw them wheel you in about an hour or so after I woke up in here, and I didn't really recognize it was you at first, though considering what this place is apparently designed to do that's not all too surprising."

"What do you mean?" Ben asked, trying to stop Eugene's rambling so he could get a clear answer.

"Well I don't have all the details but as far as I can tell th-"

Eugene paused rather abruptly, causing Ben to feel a small knot form in his stomach. He couldn't see anyone else behind the curtain, though they may have just been too far away for the light to reflect properly against the clothe that separated him from his friend.

"Hey what's up Doc?" he heard Eugene say, addressing the new arrival.

"I do hope I'm not interrupting anything for you boys," said a thick Irish accent.

"Hey, you're that guy from before!" Ben yelled out across the room, though he instantly regretted it as the same acidic feeling welled up in his throat.

"If yer referring to me boyo, you're correct. Now, as you both were discussing, welcome to Project Recycle."

Ben felt his muscle tense up as he instantly forgot about his previous physical displeasure. He didn't like the sound of the word 'project' here. If this was anything like Project Freelancer, both he and Eugene could be in serious trouble.

Suddenly, the curtain pulled back, revealing a rather tall man with streaking red hair who had the appearance of a man on the lower end of middle aged. Ben shot the man a suspicious glare. Though he couldn't see much of Eugene from here, he knew his friend was in a bed similar to his.

"Now I'm sure you have a lot of questions, but if we remain calm I'm sure we can get through them." Yet again, the doctors' voice seemed to have a soothing effect on the man.

Ben leaned back, seeming to be deep in thought. "Alright, let's keep this simple for now," he finally said, relying on his training to remain calm as he searched for answers. "I'll ask a question and you answer, alright?"

"Very well, ask away," the doctor agreed.

"First question, what is Project Recycle?"

"Project Recycle is a Special Operations program funded by the Samson Initiative designed to bring back notable soldiers and personnel from all branches of the UNSC in fighting condition," he rattled off the rehearsed explanation, sounding like a pamphlet at a seminar. "Although Project Recycle has several other minor functions, it is purely a research based program, if that's what you're worried about," He said in a joking manner.

"Alright…" Ben said slowly, absorbing the words as he formed his next question. "How does this work, exactly? Last thing I remember, I thought I was dying. Did you… use some new medical procedure to save us?"

"Ah, now that's the fun part. Taking a heavy sample of your DNA, we were able to create a hybrid-flash clone of your body, then making sure there were no special abnormalities to take care of; we injected several types of stem cells into the clone in order to make sure there would be no nasty genetic based problems in the future. Though there has proven to be some minor side effects to this, such as cellular regression, muscle memory loss, loss of muscle mass, small things like that that can be fixed over time."

The doctor paused to inhale before continuing.

"Now the tricky part was getting that wonderful brain of yours back together, and thankfully in your case we were able to find various bits of brain matter at the site of your death, most of which contained neural relays with bits of your memory. The rest we patched together using old records, various video feeds etcetera. Sadly, your friend over there had to have a bit more patch work done to him so he may not remember everything, though over time and with the correct input, hey may form his own memories of what happen."

Nearly everything the doctor said to Ben was lost on him, biology wasn't his strong suit. Though from the bits and pieces he was able to comprehend, Ben was able to figure out his next question.

"So, we're clones?" Ben said, trying to filter the doctor's words into something he could understand.

"More or less," the red head answered, shrugging.

Ben took a deep breath. A large part of him was trying to panic at the news, but he fought it down. Now wasn't the time. He needed more answers.

"Alright. I think I understand some of what's going on now. What was that you were saying about side effects earlier? They sound like they could be a problem."

Letting out a hearty laugh, the doctor quickly responded with an accompanying dismissive hand gesture. "Not at all boyo, in short, it just means that your body has been physically regressed into your early twenties, I'd guess around 22 or 23 by the look of yer face."

Ben must have had shock written all over him because the doctor quickly handed him a mirror.

The first thing Ben noticed was his eye. It was perfect; no scar, no discoloration, nothing. He was so surprised by this it took him a moment to see the rest of his face. It was true; he was biologically in his early twenties. Shock aside, Ben continued on with his interrogation.

"Doc, I got one last question," he said, setting down the mirror. "Why us? We're just a couple of old war criminals."

The older man was about to respond when a female dressed in blue scrubs rushed into the room and whispered something into his ear. Whatever it was, it wasn't good news as a grim look sprouted on the doctors' face.

"A-ah…I'm sorry gentlemen, it seems I'll have to answer your questions another time." He said as he swiftly left the recovery room.

Ben could only lay there stunned, trying to piece together all the new information he had acquired. It was unreal, both of them had died, only to be brought back and given new bodies. He had to double check to make sure it was really his body.

Picking up the mirror, he hashed a glance at the reflective device only to be reassured that it was indeed him. Brown hair, brown eyes, square jaw, everything was just as it was, but younger. He felt like he was looking at his college yearbook.

"Ben, if you keep looking at the mirror, you might crack it."

"Wha…oh...hehe, yea I guess so. It's just unreal ya know? I mean one minute I'm slipping into deaths harsh embrace, the next I'm awake and alive in a hospital bed."

"I know what you mean, though I'm still trying to piece everything back together myself," Eugene said in a simplistic tone. "I'm not sure whether I'm lucky or not that I don't remember my own death."

"Take it from me," York said, voice far away for a brief moment. "You're lucky."

Ben let out a sigh as he drew his mind away from the memory and looked around the room, taking in his new surroundings. On the wall adjacent to his bed, there was a holo-clock, displaying the time which by local standards was fairly late. The room didn't have any windows sadly, so the clock was all he had to go on. Like most hospitals, or in this case, a recovery room. Looking to his right, he was greeted with the sight of hospital bed bars, which seemed to enjoy obscuring his vision and given that he couldn't sit up straight at that moment, he had to settle with glaring at it.

He couldn't see Eugene's face yet, but if what the doctor told him was correct, then it was safe to assume that his friend was in the same physical condition. He tried to imagine what a younger Eugene would look like, before giving up. He'd just have to wait and see.

"Hey Ben?" the other man's voice broke into his musings.

"Yea?" Ben asked.

"What's the Samson Initiative?"

"Well," Ben said thoughtfully, trying to remember. "I don't know much about it myself, but from what I was able to figure out during out during my travels it was a program designed to provide funding to various research projects, like our own, during the war. You remember that Chairman the Director used to always complain was breathing down his neck?"

"Yeah," Eugene answered.

"Well, he was in charge of keeping an eye on the project," Ben explained. "Y'know, make sure they were using the money properly and all that."

"Oh," Eugene said thoughtfully. "Hey Ben?"

"Yeah?" Ben asked again.

"I think somebody should fire that Chairman guy," Eugene said. Ben could hear the grin in his voice even from here.

"Think you might be right about that," Ben agreed.

Before their conversation could continue, a nurse walked into the room, the same one from before who had on the blue scrubs. Since Eugene was closest to the door, she went to him first. Reaching down, the nurse pushed down a small cotton ball against the man's arm while simultaneously pulling the needle out. Instantly the cotton ball started to soak up the blood as the nurse held it there for well over a minute.

Walking over to Ben, she repeated the same process, though Ben couldn't help but make a small grunting noise when the needle was removed. He hated needles.

"Please follow me when you're fully changed," the nurse instructed before stepping out the door.

Casting his gaze over to Eugene, Ben saw that he was already up and out of bed. He glanced down at the foot of his bed and saw a basic uniform waiting for him. Quickly pulling on the green t-shirt, digital-camo pants, and combat boots, the pair quickly hustled outside where the nurse was waiting. Without saying a word, the nurse led them out of the medical bay, passing several rooms on the way, one of which Ben recognized as the surgery room. Minutes passed before the woman stopped in front of a sealed door, only to quickly whisk herself away back towards the medical bay.

"After you, Eugene," Ben offered, gesturing to the door.

However, before either man could make a move, the door opened, revealing the strange Irish doctor from before.

"Laddies, welcome," he greeted them distractedly. "I'm sorry to say we don't have much time," he said before practically pushing both of the men inside the room.

"I need to keep this rather short," the doctor continued once the door was closed. Time is of the essence. Project Recycle is one of the few remaining Special Operation programs left over from the war that is still active and being funded. Now, a long time ago there was another project, one that had the potential to be more dangerous than Project Imbalance, the Spartan Program or Project Freelancer. Its name was Project Heretic."

The doctor paused briefly, expecting to see some sort of reaction from the two men. All he received was confusion.

"It was designed to keeping mentally unstable soldiers with greatly needed skills in the field," he explained, "often paired with brainwashed covenant forces. Many of the unmonitored agents have gone rogue, and there is a rogue faction that is seeking something in particular that you may find of personal interest, Mr. Benjamin."

The doctor paused for breath, and Ben took the opportunity to speak up. "What are they looking for?"

"They are hunting after a former Freelancer agent by the name of Carolina, or more specifically, her AI Epsilon. He may have files that the UNSC needs desperately and the Faction is willing to do anything to get it. This is the reason you were brought back," the doctor explained. "We know where she is, but the UNSC doesn't have the man power to spare to go after her, so we thought you might be more….willing."

Ben was in shock. She was alive, after all these years. He almost couldn't believe it, was prepared to call this man a liar, except he knew. If anyone could have survived, it'd have been Carolina. He could hardly think from his joy, but he felt the words leave his mouth.

"I'll do it."

His reaction seemed to surprise the doctor, who had expected demands for further explanation and mistrust at his words. Eugene, however, wasn't shocked at all. He knew Ben would do or believe anything to get her back.

"If he's going, so am I," Eugene said. "I might not be as good without my sister guarding my back, but I can't let the locksmith go alone." Ben gave him a thankful smile, and he nodded in response.

"Very well, then," the doctor said happily. "We're glad to have you aboard, Agents New York and North Dakota. Welcome to Project Recycle."


End file.
